D&D - or, more accurately but much less tractable, its influence - is certainly holding back the CRPG-industry from unexplored new vistas. And it is doing this not because it is a bad system, and not because it does not lend itself to adpation to the PC either. It does it because it, and its clones, are definitely overused and have burned a too one-dimensional idea of RPGs into the minds of the gaming community.
Any system is useful for some kinds of game, and worthless for others. D&D is useful for heroic games with lots of fighting, with archetypical inhabitants - and this can be fun. But that doesn't mean it can be used to play psychological gothic horror with it. You could try, but you would get something much less than perfect, as you would be fighting against the system. A system should do some positive things for you, in terms of atmosphere, relevant fleshing out of the character, etcetera. In a psychological gothic horror game (think of Poe), what use a Strength-stat? It would be superfluous. Worse: what use experience and 'level up'? It would destroy the kind of game you are trying to make. As long as one is trapped within the confines of D&D-like mechanics, there will be no RPGs of gothic horror. (Fighting undead is _not_, I'd like to stress, gothic horror.) This is only one of the unexplored vistas I alluded to above.
It is important to understand that system _does_ matter. D&D3E is perfect for running adungeon-crawl campaign where an ever stronger band of heroes of goodness cleanses an entire realm of the followers of some evil cult. It is the classic RPG-session: the DM has prepared a dungeon full of foes and traps, and the players muts use all their powers to make it through alive. This has been the model for most every CRPG. (There have been exceptions.) But if you and your players are in for a night of deep stroytelling, investigating philosophical themes through concrete narration, developing interesting and rich characters - well, don't bother with D&D. It's not going to help you, it's going to hinder you. Use something like The Pool (http://www.randomordercreations.com/thepool.html) instead. But don't use The Pool for the previously described campaign of heroic fighting - that would be a disaster.
My point is of course that there is much ground beyond the tired old "heroes of goodness kick the butt of evil monsters"-games, the theme of which never seems to get beyond "good can overcome evil if it earns enough experience points". I'd like to draw attention to the fact that a good story has a theme as well as events; it is _about_ something beyond the events which constitue it. (The designers of Torment understood this, but they were almost alone. For instance, I truly could not play NWN because of the incredibly bad plot-writing.) Anyway, there is a world of possible roleplaying experiences, and only a fraction of that world is covered by the D&D-paradigm of heroes earning experience, getting better, and killing ever bigger monsters.